Package fr.ens.biologie.genomique.eoulsan.util.r

Class AbstractRExecutor

java.lang.Object

fr.ens.biologie.genomique.eoulsan.util.r.AbstractRExecutor

All Implemented Interfaces:

RExecutor

Direct Known Subclasses:

ProcessRExecutor, RserveRExecutor

public abstract class AbstractRExecutor
extends Object
implements RExecutor

This class define an abstract RExecutor.

Since:

2.0

Author:

Laurent Jourdren

Method Summary

Modifier and Type	Method	Description
void	closeConnection()	Close the connection.
void	executeRScript(String rScript, boolean sweave, String sweaveOutput, boolean saveRscript, String description, DataFile workflowOutputDir, String... scriptArguments)	Execute a R script.
void	executeRScript(String code, String description, DataFile workflowOutputDir)	Execute a R script.
void	getOutputFiles()	Get the output files of the analysis
void	openConnection()	Open the connection.
void	putInputFile(DataFile inputFile)	Put a file for the analysis.
void	putInputFile(DataFile inputFile, String outputFilename)	Put a file.
void	removeInputFiles()	Remove input files.

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface fr.ens.biologie.genomique.eoulsan.util.r.RExecutor

getName, writeFile

Method Details

openConnection

public void openConnection()
                    throws IOException

Description copied from interface: RExecutor

Open the connection.

Specified by:

openConnection in interface RExecutor

Throws:

IOException - if an error occurs while opening the connection

closeConnection

public void closeConnection()
                     throws IOException

Description copied from interface: RExecutor

Close the connection.

Specified by:

closeConnection in interface RExecutor

Throws:

IOException - if an error occurs while closing the connection

getOutputFiles

public void getOutputFiles()
                    throws IOException

Description copied from interface: RExecutor

Get the output files of the analysis

Specified by:

getOutputFiles in interface RExecutor

Throws:

IOException - if an error occurs while getting the output files

putInputFile

public void putInputFile(DataFile inputFile)
                  throws IOException

Description copied from interface: RExecutor

Put a file for the analysis.

Specified by:

putInputFile in interface RExecutor

Parameters:

inputFile - the input file

Throws:

IOException - if an error occurs while putting the file

putInputFile

public void putInputFile(DataFile inputFile,
 String outputFilename)
                  throws IOException

Description copied from interface: RExecutor

Put a file.

Specified by:

putInputFile in interface RExecutor

Parameters:

inputFile - the file to put

outputFilename - the output filename

Throws:

IOException - if an exception occurs while putting a file

removeInputFiles

public void removeInputFiles()
                      throws IOException

Description copied from interface: RExecutor

Remove input files.

Specified by:

removeInputFiles in interface RExecutor

Throws:

IOException - if an error occurs while removing the files

executeRScript

public void executeRScript(String rScript,
 boolean sweave,
 String sweaveOutput,
 boolean saveRscript,
 String description,
 DataFile workflowOutputDir,
 String... scriptArguments)
                    throws IOException

Description copied from interface: RExecutor

Execute a R script.

Specified by:

executeRScript in interface RExecutor

Parameters:

rScript - the source of the script to execute

sweave - true if the script is a Sweave script

sweaveOutput - Sweave output file

saveRscript - true to keep the R script

description - description of the R script

workflowOutputDir - workflow output directory

scriptArguments - script arguments

Throws:

IOException - if an error occurs while executing the script

executeRScript

public void executeRScript(String code,
 String description,
 DataFile workflowOutputDir)
                    throws IOException

Description copied from interface: RExecutor

Execute a R script.

Specified by:

executeRScript in interface RExecutor

Parameters:

code - code to execute

description - description of the R script

workflowOutputDir - workflow output directory

Throws:

IOException - if an error occurs while executing the script